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OPENSEQ.org
cIp_3_4_cIV_C_4
Genes: A B A+B
Length: 674 274 923
Sequences: 1936 2893 420
Seq/Len: 2.87 10.56 0.46
MirrorTree (Pazo et al. 2001) 0.13
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.01 0.00 0.01
10 0.01 0.00 0.02
20 0.01 0.00 0.03
100 0.03 0.00 0.08
∞ 0.09 0.01 0.44
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
135_Y 19_F 1.34 0.42 0.00
9_I 271_I 1.23 0.34 0.00
301_P 177_I 1.22 0.34 0.00
84_I 32_A 1.22 0.33 0.00
377_L 116_P 1.14 0.28 0.00
426_L 11_I 1.13 0.28 0.00
8_K 211_Y 1.13 0.28 0.00
248_K 139_W 1.13 0.27 0.00
233_I 36_M 1.13 0.27 0.00
324_V 103_V 1.04 0.22 0.00
398_S 189_L 1.03 0.22 0.00
9_I 21_G 1.02 0.21 0.00
84_I 22_A 1.01 0.21 0.00
580_I 187_T 0.99 0.20 0.00
508_V 211_Y 0.97 0.19 0.00
70_V 148_I 0.96 0.19 0.00
5_R 24_G 0.95 0.18 0.00
380_T 108_A 0.94 0.18 0.00
12_T 223_I 0.93 0.17 0.00
14_I 27_V 0.92 0.17 0.00
393_I 69_D 0.92 0.17 0.00
316_I 39_I 0.92 0.17 0.00
151_V 53_L 0.91 0.17 0.00
570_A 151_L 0.91 0.16 0.00
241_S 62_V 0.90 0.16 0.00
575_K 209_A 0.90 0.16 0.00
177_M 205_V 0.89 0.16 0.00
55_V 54_I 0.89 0.15 0.00
313_G 167_G 0.89 0.15 0.00
241_S 209_A 0.88 0.15 0.00
233_I 24_G 0.88 0.15 0.00
232_S 189_L 0.88 0.15 0.00
419_V 22_A 0.87 0.15 0.00
470_N 208_G 0.87 0.15 0.00
313_G 180_V 0.86 0.14 0.00
596_S 138_P 0.86 0.14 0.00
330_F 167_G 0.85 0.14 0.00
28_M 205_V 0.85 0.14 0.00
318_G 137_D 0.84 0.14 0.00
216_K 266_F 0.84 0.14 0.00
147_L 21_G 0.84 0.14 0.00
305_E 188_G 0.84 0.14 0.00
72_D 141_L 0.83 0.14 0.00
533_R 52_F 0.83 0.14 0.00
299_S 136_F 0.83 0.13 0.00
318_G 99_V 0.83 0.13 0.00
188_I 24_G 0.83 0.13 0.00
22_L 28_M 0.82 0.13 0.00
233_I 51_M 0.82 0.13 0.00
366_I 144_I 0.82 0.13 0.00
546_C 76_T 0.81 0.13 0.00
445_V 57_V 0.81 0.13 0.00
71_K 208_G 0.81 0.13 0.00
30_G 212_M 0.81 0.12 0.00
405_L 176_L 0.80 0.12 0.00
89_P 29_L 0.80 0.12 0.00
4_L 202_A 0.80 0.12 0.00
135_Y 92_I 0.80 0.12 0.00
575_K 22_A 0.80 0.12 0.00
506_E 90_G 0.80 0.12 0.00
22_L 22_A 0.79 0.12 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
4015 0.46 cIp_3_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4013 0.38 cIp_3_40_cIV_C_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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